conserved and variable functions of the σe stress response in related genomes守恒的和可变的功能σe应激反应相关基因.pdfVIP

PLoS BIOLOGY Conserved and Variable Functions of the rE Stress Response in Related Genomes 1 1¤a 1¤b 1 1,2* Virgil A. Rhodius , Won Chul Suh , Gen Nonaka , Joyce West , Carol A. Gross 1 Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America, 2 Department of Cell and Tissue Biology, University of California, San Francisco, California, United States of America Bacteria often cope with environmental stress by inducing alternative sigma (r) factors, which direct RNA polymerase to specific promoters, thereby inducing a set of genes called a regulon to combat the stress. To understand the conserved and organism-specific functions of each r, it is necessary to be able to predict their promoters, so that their regulons can be followed across species. However, the variability of promoter sequences and motif spacing makes E their prediction difficult. We developed and validated an accurate promoter prediction model for Escherichia coli r , which enabled us to predict a total of 89 unique rE-controlled transcription units in E. coli K-12 and eight related genomes. rE controls the envelope stress response in E. coli K-12. The portion of the regulon conserved across genomes is functionally coherent, ensuring the synthesis, assembly, and homeostasis of lipopolysaccharide and outer membrane porins, the key constituents of the outer membrane of Gram-negative bacteria. The larger va